Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

Ismael A Vergara1, Maja Tarailo-Graovac1, Christian Frech1, Jun Wang1, Zhaozhao Qin1, Ting Zhang1, Rong She2, Jeffrey SC Chu1, Ke Wang2 and Nansheng Chen12*

  • * Corresponding author: Nansheng Chen chenn@sfu.ca

  • † Equal contributors

Author Affiliations

1 Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada

2 School of Computing Science, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada

For all author emails, please log on.

BMC Genomics 2014, 15:255  doi:10.1186/1471-2164-15-255

Published: 2 April 2014

Abstract

Background

Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species.

Results

Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains.

Conclusions

The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains.

Keywords:
C. elegans; Natural isolate strain; Next-generation DNA sequencing; Genomic variation; Loss-of-function; Large insertion; Compound variation